Phosphorylation site assignment of high throughput tandem mass spectrometry (LC-MS/MS) data is one of the most common and critical aspects of phosphoproteomics. Correctly assigning phosphorylated residues helps us understand their biological significance.

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Processes localization-specific probability for every phosphorylation site within a data set. Ascore allows users to detect peptides, shows the degree of certainty and the non-localized peptides. This software can determine the proper phosphorylation site alignment by calculating the differences in site placement at the level of the site-determining ions. It avoids the potential inconsistencies that may happen from manual validation.

Enables automated and confident localization of modification sites within validated peptide sequences. ptmRS calculates individual probability values for each putatively modified site based on the given tandem mass spectrometry (MS/MS) data. It can be applied to all commonly used fragmentation techniques (CID, ETD and HCD). It also automatically adapts its processing performance to the individual system resources. ptmRS is the successor of PhoshoRS.

Discovers phosphorylated peptides and pinpoints the exact location(s) of their phosphorylation sites. PhosphoScan employs MS2 and MS3 pair information to proceed. It can analyze data generated from the mass spectrometric analysis of a known hyperphosphorylated protein and a synthetic phosphopeptide. This tool supports up to two phosphorylation sites per peptide sequence.

Automates post-translational modification (PTM) site assignment in proteomic experiments. Scaffold PTM is a program assessing site assignments for any post-transnational modification (PTM). It accepts overlapping data from different peptides simultaneously to improve confidence in specific site assignments. It utilizes the Ascore algorithm to interpret sites of modification on a peptide-by-peptide basis. This tool permits users to study the peptide interpretations into protein specific sites of modification, comprised of multiple pieces of overlapping evidence.

A tool which enables researchers to localise sites of post-translational modifications to peptides identified in mass spectrometry experiments. SLoMo caters for both high and low resolution data and allows for site-localization of any UniMod post-translational modification. SLoMo accepts input data from a variety of formats (e.g., Sequest, OMSSA). SLoMo is validated with high and low resolution ETD, ECD, and CID data.

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